Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate H281DRAFT_04155 H281DRAFT_04155 sorbitol ABC transporter ATP-binding protein /mannitol ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Burk376:H281DRAFT_04155 Length = 369 Score = 326 bits (835), Expect = 7e-94 Identities = 188/376 (50%), Positives = 240/376 (63%), Gaps = 26/376 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M ++ L NI K Y + + + + NLDI D EF+VFVGPSGCGKST +RMIAGLEDI+ G Sbjct: 1 MASVTLRNIRKAYDDTE--VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 +L I+ MND P R IAMVFQ+YALYPHM++Y+NMAFGLKL KK +I+ V AA Sbjct: 59 DLTINGTRMNDVPPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 +IL + L+RKP LSGGQRQRVA+GRAI R KVFL DEPLSNLDA LRV MR E A+ Sbjct: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H + T IYVTHDQ EAMTLAD+IV++SA G +EQ+G+P LY+ PAN+ Sbjct: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSA----------GNLEQVGSPTMLYHAPANR 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQ-EKILEEKGYL--GKKVTLGIRP 297 FVAGFIGSP MNF E V+ V DG+++ G+ +++ E G + G KVT+GIRP Sbjct: 229 FVAGFIGSPKMNFMEGVVQS---VTHDGVTVRYETGETQRVAVEPGAVKQGDKVTVGIRP 285 Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVK--FGSTEFTARVNARDSHSPGEK 355 E + H + V+A + E LG + LY + AR+ + H+ GE Sbjct: 286 EHL------HVGMTDDGVSARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHAKGET 339 Query: 356 VQLTFNIAKGHFFDLE 371 +L H FD E Sbjct: 340 QKLGATPEHCHLFDSE 355 Lambda K H 0.318 0.135 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 371 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 369 Length adjustment: 30 Effective length of query: 347 Effective length of database: 339 Effective search space: 117633 Effective search space used: 117633 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory